Application of WGS to antimicrobial resistance detection and surveillance


Kelsey Florek, MPH, PhD
2018 ARLN Regional Meeting
July 25, 2018




Slides available at:
www.k-florek.net/talks

How sequencing works


WSLH pipelines and applications


CRE sequencing project

Any sufficiently advanced technology is indistinguishable from magic.

- Arthur C. Clarke

How sequencing works

  • short read

    • 300bp max
    • millions of reads
    • 99.9999% accuracy
    • low cost per sample

  • long read

    • 2.3mb reads
    • thousands of reads
    • 98% accuracy
    • high cost per sample
Illumina.com
3402 Bioinformatics
www.pacb.com
Hill et al. Biochemical Society Transactions 2017
nanoporetech.com
nanoporetech.com

Analyzing sequencing data and reconstructing genomes

Issues with repeats and short reads

Wick RR et al. PLoS Comput Biol 2017.

WSLH pipelines and applications

Bucky-TR pipeline

Results of Bucky-TR

  • ~800 Salmonella isolates
  • ~230 E. coli isolates
  • ARLN isolates:
    • IMP-13 (Enterobacter cloacae)
    • IMP-27 (Providencia rettgeri)
    • NMC (Enterobacter cloacae)
    • IMI (Enterobacter asburiae)
    • OXA-23 (Acinetobacter baumannii)(3)
    • MIR-1 (Enterobacter cloacae)

CRE sequencing project

Conlan S et al. mBio 2016.

Summary

  • 2011 outbreak - National Institutes of Health Clinical Center
  • 19 patients
  • 2 were colonized 2-4 years
  • plasmids undergo dynamic hybridization
Conlan S et al. mBio 2016.

WLSH Study

Gain a better picture of the dynamics of
KPC resistant plasmids in Wisconsin.

  • 2011 - 2017
  • 180 total isolates
  • MinIon and PacBio
  • PCR confirmed KPC (OXA,IMP,VIM,NDM)

Questions?

amplicon sequencing

Shotgun whole-genome assembly

Shotgun whole-genome assembly